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src/main/java/edu/umn/biomedicus/gpl/penntree/PennTreebankInputFileAdapter.java
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| /* | ||
| * Copyright (C) 2016 Regents of the University of Minnesota | ||
| * | ||
| * This program is free software: you can redistribute it and/or modify | ||
| * it under the terms of the GNU General Public License as published by | ||
| * the Free Software Foundation, either version 3 of the License, or | ||
| * (at your option) any later version. | ||
| * | ||
| * This program is distributed in the hope that it will be useful, | ||
| * but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| * GNU General Public License for more details. | ||
| * | ||
| * You should have received a copy of the GNU General Public License | ||
| * along with this program. If not, see <http://www.gnu.org/licenses/>. | ||
| */ | ||
|
|
||
| package edu.umn.biomedicus.gpl.penntree; | ||
|
|
||
| import com.google.inject.Inject; | ||
| import edu.stanford.nlp.ling.TaggedWord; | ||
| import edu.stanford.nlp.trees.PennTreeReaderFactory; | ||
| import edu.stanford.nlp.trees.Tree; | ||
| import edu.stanford.nlp.trees.TreeReader; | ||
| import edu.umn.biomedicus.common.types.syntax.PartOfSpeech; | ||
| import edu.umn.biomedicus.common.types.syntax.PartsOfSpeech; | ||
| import edu.umn.biomedicus.common.types.text.ImmutableParseToken; | ||
| import edu.umn.biomedicus.common.types.text.Sentence; | ||
| import edu.umn.biomedicus.framework.store.Document; | ||
| import edu.umn.biomedicus.framework.store.Label; | ||
| import edu.umn.biomedicus.framework.store.Span; | ||
| import edu.umn.biomedicus.framework.store.TextView; | ||
| import edu.umn.biomedicus.uima.adapter.UimaAdapters; | ||
| import edu.umn.biomedicus.uima.files.InputFileAdapter; | ||
| import edu.umn.biomedicus.uima.labels.LabelAdapters; | ||
| import java.io.IOException; | ||
| import java.io.Reader; | ||
| import java.nio.file.Files; | ||
| import java.nio.file.Path; | ||
| import java.util.ArrayList; | ||
| import java.util.List; | ||
| import java.util.Random; | ||
| import org.apache.uima.cas.CAS; | ||
| import org.apache.uima.collection.CollectionException; | ||
|
|
||
| /** | ||
| * Adapts Penn treebank format files to CAS files. | ||
| * | ||
| * @author Ben Knoll | ||
| * @since 1.3.0 | ||
| */ | ||
| public final class PennTreebankInputFileAdapter implements InputFileAdapter { | ||
|
|
||
| /** | ||
| * The penn tree reader factory. | ||
| */ | ||
| private final PennTreeReaderFactory pennTreeReaderFactory = new PennTreeReaderFactory(); | ||
|
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| private final LabelAdapters labelAdapters; | ||
|
|
||
| /** | ||
| * The view name to load into. | ||
| */ | ||
| private String viewName; | ||
|
|
||
| @Inject | ||
| public PennTreebankInputFileAdapter(LabelAdapters labelAdapters) { | ||
| this.labelAdapters = labelAdapters; | ||
| } | ||
|
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||
| @Override | ||
| public void adaptFile(CAS cas, Path path) throws CollectionException { | ||
| StringBuilder text = new StringBuilder(); | ||
| ArrayList<SentenceBuilder> sentences = new ArrayList<>(); | ||
| try (Reader reader = Files.newBufferedReader(path)) { | ||
| TreeReader treeReader = pennTreeReaderFactory.newTreeReader(reader); | ||
| Tree tree; | ||
| while ((tree = treeReader.readTree()) != null) { | ||
| int sentenceStart = text.length(); | ||
|
|
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| ArrayList<TaggedWord> taggedWords = tree.taggedYield(); | ||
| SentenceBuilder sentenceBuilder = new SentenceBuilder(); | ||
| sentenceBuilder.tokenBuilders = new ArrayList<>(taggedWords.size()); | ||
| for (TaggedWord taggedWord : taggedWords) { | ||
| String tag = taggedWord.tag(); | ||
| String word = taggedWord.word(); | ||
| text.append(" "); | ||
|
|
||
| /** | ||
| * This -NONE- tag occurs in some documents when there is a assumed phrase. | ||
| */ | ||
| if (!"-NONE-".equals(tag)) { | ||
| int tokenStart = text.length(); | ||
| if ("-LRB-".equals(word)) { | ||
| text.append('('); | ||
| } else if ("-RRB-".equals(word)) { | ||
| text.append(')'); | ||
| } else if ("-LCB-".equals(word)) { | ||
| text.append('{'); | ||
| } else if ("-RCB-".equals(word)) { | ||
| text.append('}'); | ||
| } else if ("-LSB-".equals(word)) { | ||
| text.append('['); | ||
| } else if ("-RSB-".equals(word)) { | ||
| text.append(']'); | ||
| } else if ("``".equals(word)) { | ||
| text.append("\""); | ||
| } else if ("''".equals(word)) { | ||
| text.append("\""); | ||
| } else { | ||
| text.append(word); | ||
| } | ||
| int tokenEnd = text.length(); | ||
|
|
||
| PartOfSpeech partOfSpeech; | ||
| if ("-LRB-".equals(tag)) { | ||
| partOfSpeech = PartOfSpeech.LEFT_PAREN; | ||
| } else if ("-RRB-".equals(tag)) { | ||
| partOfSpeech = PartOfSpeech.RIGHT_PAREN; | ||
| } else { | ||
| if (tag.contains("|")) { | ||
| String[] tags = tag.split("\\|"); | ||
| Random random = new Random(); | ||
| int randomIndex = random.nextInt(tags.length); | ||
| partOfSpeech = PartsOfSpeech.forTag(tags[randomIndex]); | ||
| } else { | ||
| partOfSpeech = PartsOfSpeech.forTag(tag); | ||
| } | ||
|
|
||
| } | ||
|
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| TokenBuilder tokenBuilder = new TokenBuilder(); | ||
| tokenBuilder.tokenSpan = new Span(tokenStart, tokenEnd); | ||
| tokenBuilder.partOfSpeech = partOfSpeech; | ||
| if (partOfSpeech == null) { | ||
| throw new AssertionError("part of speech should not be null"); | ||
| } | ||
| sentenceBuilder.tokenBuilders.add(tokenBuilder); | ||
| } | ||
| } | ||
|
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| int sentenceEnd = text.length(); | ||
|
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| sentenceBuilder.sentenceSpan = new Span(sentenceStart, sentenceEnd); | ||
| sentences.add(sentenceBuilder); | ||
| } | ||
| } catch (IOException e) { | ||
| throw new CollectionException(e); | ||
| } | ||
|
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||
| Document document = UimaAdapters.createDocument(cas, labelAdapters, | ||
| path.getFileName().toString()); | ||
| TextView textView = document.newTextView() | ||
| .withText(text.toString()) | ||
| .withName(viewName) | ||
| .build(); | ||
|
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| for (SentenceBuilder sentence : sentences) { | ||
| Span sentenceSpan = sentence.sentenceSpan; | ||
|
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| textView.label(Label.create(sentenceSpan, Sentence.create())); | ||
|
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| for (TokenBuilder tokenBuilder : sentence.tokenBuilders) { | ||
| Span tokenSpan = tokenBuilder.tokenSpan; | ||
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| textView.label(Label.create(tokenSpan, | ||
| ImmutableParseToken.builder() | ||
| .text(tokenSpan.getCovered(text).toString()) | ||
| .hasSpaceAfter(true) | ||
| .build() | ||
| )); | ||
|
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| PartOfSpeech partOfSpeech = tokenBuilder.partOfSpeech; | ||
| if (partOfSpeech != null) { | ||
| String pos = partOfSpeech.toString(); | ||
| textView.label(Label.create(tokenSpan, PartsOfSpeech.forTag(pos))); | ||
| } | ||
| } | ||
| } | ||
|
|
||
| } | ||
|
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| @Override | ||
| public void setTargetView(String viewName) { | ||
| this.viewName = viewName; | ||
| } | ||
|
|
||
| /** | ||
| * Used to build sentences. | ||
| */ | ||
| private static class SentenceBuilder { | ||
|
|
||
| /** | ||
| * The begin and end of the sentence. | ||
| */ | ||
| private Span sentenceSpan; | ||
|
|
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| /** | ||
| * The tokens of the sentence. | ||
| */ | ||
| private List<TokenBuilder> tokenBuilders; | ||
| } | ||
|
|
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| /** | ||
| * Used to build tokens | ||
| */ | ||
| private static class TokenBuilder { | ||
|
|
||
| /** | ||
| * The begin and end of the token | ||
| */ | ||
| private Span tokenSpan; | ||
|
|
||
| /** | ||
| * The part of speech. | ||
| */ | ||
| private PartOfSpeech partOfSpeech; | ||
| } | ||
| } |
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